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Sample GSM4469946 Query DataSets for GSM4469946
Status Public on Jul 28, 2020
Title G4_d4_Cy5-PDS_1uM_plus_3uM_BMVC_comp_rep2
Sample type RNA
Source name 1uM Cy5-PDS + 3uM BMVC, G4 design 4
Organism synthetic construct
Characteristics molecule name: 1uM Cy5-PDS + 3uM BMVC
dna type: ssDNA
array treatment: 100mM KCl
Treatment protocol Microarrays were preincubated with a 100mM potassium chloride solution for 1 hour at room temperature to induce G4 formation. Binding experiments were then performed as previously described in Ray et al. ACS Chem Bio 2020.
Extracted molecule other
Extraction protocol N/A
Label Cy5
Label protocol Synthesis of Cy5-labeled pyridostatin (Cy5-PDS) is described in (Ray et al., 2020).
Hybridization protocol Microarrays were blocked with 4% non-fat dry-milk in a potassium phosphate buffer before incubation with small molecules. The binding reactions (Cy5-PDS, Cy5-PDS+BMVC, or Cy5-PDS+PDS) were carried out in a hydration chamber for 1 hour followed by one wash with 0.5% Tween-20 in 1xPBS. Finally array slides were washed and dried in 1x PBS and scanned using an Agilent Sure Scan II scanner.
Scan protocol Molecule-bound microarrays were scanned with the G5761A SureScan Dx Microarray Scanner System (Agilent) to detect Cy5 signal at two laser settings (30 and 100PMT) to ensure signal intensities were below saturation. Spot intensities from microarray images were extracted using the Agilent Feature Extraction Software and are reported as raw fluorescence units. Microarrays with the fewest number of saturated spots were used for further analysis.
Description 1uM Cy5-PDS + 3uM BMVC G4 array experiment, ssDNA + 100mM KCl
Data processing An intensity value was calculated for each target sequence by computing the median signal intensity across probes containing an identical probe identifier (ProbeID)
Submission date Apr 09, 2020
Last update date Jul 29, 2020
Contact name Desiree Tillo
Phone +1-240-760-7289
Organization name NIH/NCI
Street address 41 Center Dr, Room D310
City Bethesda
State/province MD
ZIP/Postal code 20892
Country USA
Platform ID GPL28372
Series (1)
GSE148419 Custom DNA microarrays reveal the selective recognition of BMVC to MYC promoter G-quadruplex: a large-scale assessment of ligand binding selectivity

Data table header descriptions
VALUE The median fluorescence intensity of the target sequence.

Data table
D4_00001 8476.5
D4_00002 12258
D4_00003 4139
D4_00004 10499
D4_00005 6921.5
D4_00006 4900.5
D4_00007 8409
D4_00008 4232
D4_00009 4915.5
D4_00010 12924.5
D4_00011 6022
D4_00012 14856.5
D4_00013 17792.5
D4_00014 8030
D4_00015 16689
D4_00016 2006
D4_00017 9499
D4_00018 26480
D4_00019 8312
D4_00020 7255

Total number of rows: 19249

Table truncated, full table size 276 Kbytes.

Supplementary file Size Download File type/resource
GSM4469946_G4_086005_002_100PMT_4_1uM_3uM_PDS_BMVC.raw_signal.txt.gz 3.4 Mb (ftp)(http) TXT
Processed data included within Sample table

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